Safety demonstration of a microbial species for use in the food chain: Weissella confusa

Recent Records on Bacterial Opportunistic Infections via the Dietary Route

This narrative review was aimed at identifying the opportunistic bacterial pathogens that can be transmitted by contaminated food and represent a current threat for patients particularly susceptible to infections because of underlying conditions or predisposing factors. The analysis was focused on recent case or outbreak reports and systematic reviews published in the years 2019 to 2023 and resulted in sorting 24 bacterial groups comprising the genera or species able to cause a variety of systemic or invasive infections if ingested with food or drinking water. These included both bacteria known to cause mild infections in immunocompetent persons and bacteria considered to be innocuous, which are used in food fermentation or as probiotics. No recent cases of infections transmitted through dietary routes were reported for the critical nosocomial pathogens widely found in food products, primarily Acinetobacter baumannii and Klebsiella pneumoniae. However, the very first sources of their introduction into the clinical environment still need to be established. In many instances, risky dietary habits, such as eating raw fish, seafood, raw meat, unpasteurized milk, and their derived products or the lack of control in fermentation processes, has led to the reported illnesses, pointing out the necessity to improve the hygiene of production and consumer awareness of the risks.

Biotechnological Potential and Safety Evaluation of Dextran- and Riboflavin-Producing Weisella cibaria Strains for Gluten-Free Baking

Gluten consumption causes several immunological and non-immunological intolerances in susceptible individuals. In this study, the dextran-producing Weissella cibaria BAL3C-5 and its derivative, the riboflavin-overproducing strain BAL3C-5 C120T, together with a commercial bakery yeast, were used to ferment gluten-free (GF)-doughs obtained from corn and rice flours at two different concentrations and supplemented with either quinoa, buckwheat, or chickpea to obtain laboratory-scale GF bread. The levels of dextran, riboflavin, and total flavins were determined in the fermented and breads. Both strains grew in fermented doughs and contributed dextran, especially to those made with corn plus quinoa (~1 g/100 g). The highest riboflavin (350-150 µg/100 g) and total flavin (2.3-1.75 mg/100 g) levels were observed with BAL3C-5 C120T, though some differences were detected between the various doughs or breads, suggesting an impact of the type of flour used. The safety assessment confirmed the lack of pathogenic factors in the bacterial strains, such as hemolysin and gelatinase activity, as well as the genetic determinants for biogenic amine production. Some intrinsic resistance to antibiotics, including vancomycin and kanamycin, was found. These results indicated the microbiological safety of both W. cibaria strains and indicated their potential application in baking to produce GF bread.

The Weissella and Periweissella genera: up-to-date taxonomy, ecology, safety, biotechnological, and probiotic potential

Bacteria belonging to the genera Weissella and Periweissella are lactic acid bacteria, which emerged in the last decades for their probiotic and biotechnological potential. In 2015, an article reviewing the scientific literature till that date on the taxonomy, ecology, and biotechnological potential of the Weissella genus was published. Since then, the number of studies on this genus has increased enormously, several novel species have been discovered, the taxonomy of the genus underwent changes and new insights into the safety, and biotechnological and probiotic potential of weissellas and periweissellas could be gained. Here, we provide an updated overview (from 2015 until today) of the taxonomy, ecology, safety, biotechnological, and probiotic potential of these lactic acid bacteria.

Weissella confusa N17 Derived from Loach (Misgurnus anguillicaudatus) Exhibits Promising for Further Applications in Loach Aquaculture

The application of probiotics, in aquaculture, is becoming increasingly widespread and have had positive application effects. However, reports of loach-derived probiotics are quite limited. In this study, two representative strains of lactic acid bacteria with excellent traits, namely, Weissella confusa N17 and Lactobacillus saniviri N19, were screened from the intestine of healthy loaches. W. confusa N17 and L. saniviri N19 could inhibit different common various pathogenic bacteria, especially Aeromonas spp., and were sensitive to the most common antibiotics. The survival rate of the two strains exceeded 50% after 4 h of incubation in 10% loach bile. Moreover, the two strains showed significant tolerance to trypsin. Their autoaggregation capacity and hydrophobicity were greater than 30%. In addition, the aggregation ability of both strains was higher than 30% for both A. veronii TH0426 and A. hydrophila TPS. The two strains had a high biofilm-forming ability and strong adhesion to epithelioma papulosum cyprini (EPC) cells. Scanning electron microscopy results showed that the culture supernatants of the two strains had a significantly destructive effect on A. veronii TH0426 and A. hydrophila TPS. Overall, the traits of W. confusa N17 were better than those of L. saniviri N19. Genome sequencing and analysis demonstrated a lack of virulence factor-related or drug resistance-related genes in genome N17. The diet supplemented with the W. confusa N17 strain significantly improved the resistance of loaches to A. veronii infection, and the protection rate reached 57.1%. Therefore, W. confusa N17 exhibits promising for further applications in loach aquaculture.

Differentiation between Weissella cibaria and Weissella confusa Using Machine-Learning-Combined MALDI-TOF MS

Although Weissella cibaria and W. confusa are essential food-fermenting bacteria, they are also opportunistic pathogens. Despite these species being commercially crucial, their taxonomy is still based on inaccurate identification methods. In this study, we present a novel approach for identifying two important Weissella species, W. cibaria and W. confusa, by combining matrix-assisted laser desorption/ionization and time-of-flight mass spectrometer (MALDI-TOF MS) data using machine-learning techniques. After on- and off-plate protein extraction, we observed that the BioTyper database misidentified or could not differentiate Weissella species. Although Weissella species exhibited very similar protein profiles, these species can be differentiated on the basis of the results of a statistical analysis. To classify W. cibaria, W. confusa, and non-target Weissella species, machine learning was used for 167 spectra, which led to the listing of potential species-specific mass-to-charge (m/z) loci. Machine-learning techniques including artificial neural networks, principal component analysis combined with the K-nearest neighbor, support vector machine (SVM), and random forest were used. The model that applied the Radial Basis Function kernel algorithm in SVM achieved classification accuracy of 1.0 for training and test sets. The combination of MALDI-TOF MS and machine learning can efficiently classify closely-related species, enabling accurate microbial identification.

Genome analysis revealed a repertoire of oligosaccharide utilizing CAZymes in Weissella confusa CCK931 and Weissella cibaria YRK005

Weissella bacteria are gram-positive, anaerobic, fermentative, and have probiotic potential. This study aimed to compare the genomes of W. cibaria YRK005 and W. confusa CCK931 isolated from young radish and kimchi, respectively. The genomic size of W. cibaria YRK005 and W. confusa CCK931 with GC content is 2.36 Mb (45%) and 2.28 Mb (44.67%), respectively. The genome study identified 92 and 83 CAZymes genes, respectively, for W. cibaria YRK005 and W. confusa CCK931, that are responsible for 26 and 27 glycoside hydrolases (GH) and 21 and 27 glycosyl transferases. Both species have one gene for carbohydrate esterases and three genes for carbohydrate-binding modules. The primary CAZymes found in both species that are involved in oligosaccharide utilization are GH1, GH2, GH30, GH13_30, GH13_31, GH42, GH43, and GH65. The study also details the production pathways for glycogen and folate. Both strains include a unique repertoire of genes, including hypothetical proteins, showing adaptability to diverse ecological niches and evolution over time.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-022-01232-7.

Probiotic Potential and Safety Assessment of Type Strains of Weissella and Periweissella Species

Although numerous strains belonging to the Weissella genus have been described in the last decades for their probiotic and biotechnological potential, others are known to be opportunistic pathogens of humans and animals. Here, we investigated the probiotic potential of two Weissella and four Periweissella type strains belonging to the species Weissella diestrammenae, Weissella uvarum, Periweissella beninensis, Periweissella fabalis, Periweissella fabaria, and Periweissella ghanensis by genomic and phenotypic analyses, and performed a safety assessment of these strains. Based on the results of the survival to simulated gastrointestinal transit, autoaggregation and hydrophobicity characteristics, as well as adhesion to Caco-2 cells, we showed that the P. beninensis, P. fabalis, P. fabaria, P. ghanensis, and W. uvarum type strains exhibited a high probiotic potential. The safety assessment, based on the genomic analysis, performed by searching for virulence and antibiotic resistance genes, as well as on the phenotypic evaluation, by testing hemolytic activity and antibiotic susceptibility, allowed us to identify the P. beninensis type strain as a safe potential probiotic microorganism. IMPORTANCE A comprehensive analysis of safety and functional features of six Weissella and Periweissella type strains was performed. Our data demonstrated the probiotic potential of these species, indicating the P. beninensis type strain as the best candidate based on its potential probiotic features and the safety assessment. The presence of different antimicrobial resistance profiles in the analyzed strains highlighted the need to establish cutoff values to perform a standardized safety evaluation of these species, which, in our opinion, should be mandatory on a strain-specific basis.

Comparative Genomics of Halobacterium salinarum Strains Isolated from Salted Foods Reveals Protechnological Genes for Food Applications

Archaeal cell factories are becoming of great interest given their ability to produce a broad range of value-added compounds. Moreover, the Archaea domain often includes extremophilic microorganisms, facilitating their cultivation at the industrial level under nonsterile conditions. Halophilic archaea are studied for their ability to grow in environments with high NaCl concentrations. In this study, nine strains of Halobacterium salinarum were isolated from three different types of salted food, sausage casings, salted codfish, and bacon, and their genomes were sequenced along with the genome of the collection strain CECT 395. A comparative genomic analysis was performed on these newly sequenced genomes and the publicly available ones for a total of 19 H. salinarum strains. We elucidated the presence of unique gene clusters of the species in relation to the different ecological niches of isolation (salted foods, animal hides, and solar saltern sediments). Moreover, genome mining at the single-strain level highlighted the metabolic potential of H. salinarum UC4242, which revealed the presence of different protechnological genes (vitamins and myo-inositol biosynthetic pathways, aroma- and texture-related features, and antimicrobial compounds). Despite the presence of genes of potential concern (e.g., those involved in biogenic amine production), all the food isolates presented archaeocin-related genes (halocin-C8 and sactipeptides).

Weissella and the two Janus faces of the genus

The genus Weissella belongs to the lactic acid bacteria group. It occurs naturally in foods and is a component of the human microbiome. A few Weissella species are candidate probiotics due to their potential for survival under the harsh conditions present in the gastrointestinal tract of humans and animals. Various species have also shown potential for treating and preventing periodontal disease, skin pathologies, and atopic dermatitis; some are used as starters for the fermentation of foods due to their production of exopolysaccharides; and others are used as protective cultures due to their production of weissellicin, a bacteriocin. However, a few Weissella species are opportunistic pathogens, such as W. ceti, which is the etiological agent of weissellosis, a disease in rainbow trout. Additionally, most Weissella species are intrinsically vancomycin-resistant. Thus, the Weissella genus is important from both medical and industrial points of view, and the Janus faces of this genus should be considered in any expected biotechnological applications. In this review, we present an overview of the probiotic potential and pathogenic cases of the Weissella genus reported in the literature.

The Weissella Genus: Clinically Treatable Bacteria with Antimicrobial/Probiotic Effects on Inflammation and Cancer

Weissella is a genus earlier considered a member of the family Leuconostocaceae, which was reclassified into the family Lactobacillaceae in 1993. Recently, there have been studies emphasizing the probiotic and anti-inflammatory potential of various species of Weissella, of which W. confusa and W. cibaria are the most representative. Other species within this genus include: W. paramesenteroides, W. viridescens, W. halotolerans, W. minor, W. kandleri, W. soli, W. ghanensis, W. hellenica, W. thailandensis, W. fabalis, W. cryptocerci, W. koreensis, W. beninensis, W. fabaria, W. oryzae, W. ceti, W. uvarum, W. bombi, W. sagaensis, W. kimchi, W. muntiaci, W. jogaejeotgali, W. coleopterorum, W. hanii, W. salipiscis, and W. diestrammenae. Weissella confusa, W. paramesenteroides, W. koreensis, and W. cibaria are among the few species that have been isolated from human samples, although the identification of these and other species is possible using metagenomics, as we have shown for inflammatory bowel disease (IBD) and healthy controls. We were able to isolate Weissella in gut-associated bacteria (post 24 h food deprivation and laxatives). Other sources of isolation include fermented food, soil, and skin/gut/saliva of insects/animals. With the potential for hospital and industrial applications, there is a concern about possible infections. Herein, we present the current applications of Weissella on its antimicrobial and anti-inflammatory mechanistic effects, the predisposing factors (e.g., vancomycin) for pathogenicity in humans, and the antimicrobials used in patients. To address the medical concerns, we examined 28 case reports focused on W. confusa and found that 78.5% of infections were bacteremia (of which 7 were fatal; 1 for lack of treatment), 8 were associated with underlying malignancies, and 8 with gastrointestinal procedures/diseases of which 2 were Crohn’s disease patients. In cases of a successful resolution, commonly administered antibiotics included: cephalosporin, ampicillin, piperacillin-tazobactam, and daptomycin. Despite reports of Weissella-related infections, the evolving mechanistic findings suggest that Weissella are clinically treatable bacteria with emerging antimicrobial and probiotic benefits ranging from oral health, skin care, obesity, and inflammatory diseases to cancer.

Fermentation Conditions Affect the Synthesis of Volatile Compounds, Dextran, and Organic Acids by Weissella confusa A16 in Faba Bean Protein Concentrate

Fermentation with Weissella confusa A16 could improve the flavor of various plant-based sources. However, less is known about the influence of fermentation conditions on the profile of volatile compounds, dextran synthesis and acidity. The present work investigates the synthesis of potential flavor-active volatile compounds, dextran, acetic acid, and lactic acid, as well as the changes in viscosity, pH, and total titratable acidity, during fermentation of faba bean protein concentrate with W. confusa A16. A Response Surface Methodology was applied to study the effect of time, temperature, dough yield, and inoculum ratio on the aforementioned responses. Twenty-nine fermentations were carried out using a Central Composite Face design. A total of 39 volatile organic compounds were identified: 2 organic acids, 7 alcohols, 8 aldehydes, 2 alkanes, 12 esters, 3 ketones, 2 aromatic compounds, and 3 terpenes. Long fermentation time and high temperature caused the formation of ethanol and ethyl acetate and the reduction of hexanal, among other compounds linked to the beany flavor. Levels of dextran, acetic acid, and lactic acid increased with increasing temperature, time, and dough yield. Optimal points set for increased dextran and reduced acidity were found at low temperatures and high dough yield. Such conditions would result in hexanal, ethyl acetate and ethanol having a relative peak area of 35.9%, 7.4%, and 4.9%, respectively.

Microbiota analysis for risk assessment: evaluation of hazardous dietary substances and its potential role on the gut microbiome variability and dysbiosis

The expansion of fields related to probiotics, microbiome‐targeted interventions and an evolving landscape for implementation across policy, industry and end users, signifies an era of important clinical translational changes. Characteristics and perception of traditional probiotics stemmed from the historical long‐term use of fermented products. Although the distinction between probiotic microorganisms and fermentation‐associated microbes is important, it is often confused as not all fermented foods are probiotic supplements. Current innovation in area of biotechnology and bioinformatics is emerging outside of the classical definitions and new probiotics will emerge from novel sources, challenging scientific as well as regulatory instructions. At the same time, the search for individual and group microbiome signatures – biomarkers in order to predict disease incidence, progression and response to treatment is a key area of microbiological and multidisciplinary research, enabled by efficient and powerful processing of large data sets. However, the regulation of marketed beneficial microbes and probiotics differs among countries and the basic level of classification, which depend on probiotic classification is not globally harmonised. At the same time, the regulation is very demanding to evaluate the safety of products on the market, so that only those products with scientific evidence benefits can obtain positive recognition in ways of health claims. Collaborative experimental and theoretical approaches and case studies have assisted the progress in this crosscutting area of research. There is a requirement to clearly specify criteria and provide details about ways and approaches of achieving those criteria with the intention that manufacturers can benefit from a transparent way of communicating product quality to end users.

Complete Genome Sequence of Weissella confusa LM1 and Comparative Genomic Analysis

The genus Weissella is attracting an increasing amount of attention because of its multiple functions and probiotic potential. In particular, the species Weissella confusa is known to have great potential in industrial applications and exhibits numerous biological functions. However, the knowledge on this bacterium in insects is not investigated. Here, we isolated and identified W. confusa as the dominant lactic acid bacteria in the gut of the migratory locust. We named this strain W. confusa LM1, which is the first genome of an insect-derived W. confusa strain with one complete chromosome and one complete plasmid. Among all W. confusa strains, W. confusa LM1 had the largest genome. Its genome was the closest to that of W. confusa 1001271B_151109_G12, a strain from human feces. Our results provided accurate evolutionary relationships of known Weissella species and W. confusa strains. Based on genomic analysis, the pan-genome of W. confusa is in an open state. Most strains of W. confusa had the unique genes, indicating that these strains can adapt to different ecological niches and organisms. However, the variation of strain-specific genes did represent significant correlations with their hosts and ecological niches. These strains were predicted to have low potential to produce secondary metabolites. Furthermore, no antibiotic resistance genes were identified. At the same time, virulence factors associated with toxin production and secretion system were not found, indicating that W. confusa strains were not sufficient to perform virulence. Our study facilitated the discovery of the functions of W. confusa LM1 in locust biology and their potential application to locust management.

Design of a "Clean-Label" Gluten-Free Bread to Meet Consumers Demand

The market of gluten-free (GF) products has been steadily increasing in last few years. Due to the technological importance of gluten, the GF food production is still a challenge for the industry. Indeed, large quantities of fat, sugars, structuring agents, and flavor enhancers are added to GF formulations to make textural and sensorial characteristics comparable to conventional products, leading to nutritional and caloric intake imbalances. The formulation of the novel "clean-label" GF bread included a commonly used mixture of maize and rice flour (ratio 1:1) fortified with selected protein-rich flours. Naturally hydrocolloids-containing flours (psyllium, flaxseed, chia) were included in the bread formulation as structuring agents. A type-II sourdough was obtained by using a selected Weissella cibaria P9 and a GF sucrose-containing flour as substrate for fermentation to promote the exo-polysaccharides synthesis by the starter lactic acid bacterium. A two-step protocol for bread-making was set-up: first, the GF sourdough was fermented (24 h at 30 °C); then, it was mixed with the other ingredients (30% of the final dough) and leavened with baker's yeast before baking. Overall, the novel GF bread was characterized by good textural properties, high protein content (8.9% of dry matter) and in vitro protein digestibility (76.9%), low sugar (1.0% of dry matter) and fat (3.1% of dry matter) content, and an in vitro predicted glycemic index of 85.